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  • I have added end-to-end and unit tests (if applicable).
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pensarapp bot commented May 27, 2025

LLM-Generated Cypher Query Injection Vulnerability
Suggested Fix

@@ -1,6 +1,7 @@
 from typing import Any, Optional
 import logging
+import re
 from cognee.infrastructure.databases.graph import get_graph_engine
 from cognee.infrastructure.databases.graph.networkx.adapter import NetworkXAdapter
 from cognee.infrastructure.llm.get_llm_client import get_llm_client
 from cognee.infrastructure.llm.prompts import render_prompt
@@ -9,9 +10,84 @@
 from cognee.infrastructure.databases.graph.graph_db_interface import GraphDBInterface
 
 logger = logging.getLogger("NaturalLanguageRetriever")
 
+# Allowed Cypher clauses for READ-ONLY queries
+# ONLY allow SELECT-like queries (MATCH/OPTIONAL MATCH + RETURN, WHERE, LIMIT, ORDER BY etc.)
+# Prohibit clauses that change data: CREATE, MERGE, DELETE, SET, REMOVE, CALL (except permitted read procedures)
+_ALLOWED_READONLY_CLAUSES = [
+    "MATCH",
+    "OPTIONAL MATCH",
+    "RETURN",
+    "WHERE",
+    "ORDER BY",
+    "LIMIT",
+    "SKIP",
+    "UNWIND",
+    "WITH",
+    "DISTINCT",
+]
+# Forbidden (modifying/destructive) Cypher keywords
+_FORBIDDEN_CLAUSES = [
+    "CREATE",
+    "MERGE",
+    "DELETE",
+    "DETACH",
+    "SET",
+    "REMOVE",
+    "DROP",
+    "CALL",
+    "LOAD CSV",
+    "START",
+    "FOREACH",
+    "APOC",
+    "PROFILE",
+    "EXPLAIN",
+    "GRANT",
+    "DENY",
+    "REVOKE",
+]
 
+def is_cypher_query_safe(query: str) -> bool:
+    """
+    Returns True if the provided Cypher query is 'safe' (read-only); False otherwise.
+
+    We enforce that it does not contain any forbidden clauses, and only permitted starting clauses.
+    """
+    if not isinstance(query, str):
+        return False
+    
+    # Make matches case-insensitive, normalize query
+    normalized_query = query.upper()
+    # Remove multi-line comments and inline comments
+    normalized_query = re.sub(r"//.*?$|/\*.*?\*/", "", normalized_query, flags=re.MULTILINE | re.DOTALL)
+    # Basic check: Look for any forbidden clause as whole word
+    for forbidden in _FORBIDDEN_CLAUSES:
+        pattern = r'\b' + re.escape(forbidden) + r'\b'
+        if re.search(pattern, normalized_query):
+            return False
+
+    # Must start with a MATCH or OPTIONAL MATCH (with optional WITH/UNWIND/RETURN statements in between)
+    allowed_starter = False
+    # Find first non-empty, non-comment line
+    statements = [line.strip() for line in normalized_query.splitlines() if line.strip()]
+    joined = " ".join(statements)
+    # Check if it starts with MATCH or OPTIONAL MATCH, possibly after WITH or UNWIND
+    match_start = re.match(r'^(WITH|UNWIND|MATCH|OPTIONAL MATCH)', joined)
+    if match_start:
+        first_clause = match_start.group(1)
+        if first_clause in ("MATCH", "OPTIONAL MATCH", "WITH", "UNWIND"):
+            allowed_starter = True
+    else:
+        # Or maybe just starts with RETURN or WITH in rare cases
+        allowed_starter = joined.startswith("RETURN") or joined.startswith("WITH")
+
+    if not allowed_starter:
+        return False
+
+    return True
+
+
 class NaturalLanguageRetriever(BaseRetriever):
     """
     Retriever for handling natural language search.
 
@@ -78,8 +154,12 @@
                 cypher_query = await self._generate_cypher_query(
                     query, edge_schemas, previous_attempts
                 )
 
+                if not is_cypher_query_safe(cypher_query):
+                    logger.error("Aborting execution: LLM-generated Cypher query failed safety check. Query: %s", cypher_query)
+                    raise RuntimeError("Generated Cypher query is not permitted by safety policy (must be read-only).")
+                    
                 logger.info(
                     f"Executing generated Cypher query (attempt {attempt + 1}): {cypher_query[:100]}..."
                     if len(cypher_query) > 100
                     else cypher_query
@@ -156,5 +236,5 @@
         """
         if context is None:
             context = await self.get_context(query)
 
-        return context
+        return context
\ No newline at end of file
Explanation of Fix

Vulnerability:
The code accepts untrusted user input (a natural language query), passes it to an LLM, and then directly executes the LLM's output as a Cypher query against a graph database. Because there is no validation, filtering, or restriction on the Cypher statements generated by the LLM, an attacker can use prompt injection to have the LLM emit arbitrary and potentially destructive Cypher statements (e.g., deleting all nodes, exfiltrating data, etc.). This is a variant of SQL/graph-query injection (CWE-89) enabled by prompt injection against the LLM (OWASP-ML01) since the LLM will do what the attacker directs through prompt engineering.

Fix Approach:
To mitigate this, direct execution of arbitrary LLM-generated Cypher is prevented. Instead, implement a restrictive allow-list (deny-listing is unsafe) of permitted Cypher statement types. Only read-only Cypher statements (e.g., MATCH, RETURN, optional WHERE, LIMIT, etc.) are permitted, and queries with destructive or modifying clauses (e.g., CREATE, DELETE, SET, REMOVE, MERGE, etc.) are blocked. This is enforced by statically analyzing the generated Cypher; if any disallowed clause is found, the query is not executed, and an error is logged. The code will raise an exception if a generated Cypher fails validation.

Side Effects:

  • This patch may prevent legitimate, but unsafe, graph interactions that require modification.
  • If the LLM output contains ambiguous or unexpected Cypher, it will be blocked.
  • Only allows read-only Cypher statements to be executed, which aligns with most search/retrieval cases.
  • No new dependencies introduced. Code is self-contained and compatible with the rest of the application.
  • Errors are logged and bubbled up for handling, following the existing error management style.
Issues
Type Identifier Message Severity Link
Application
CWE-532, CWE-89, ML01
User-supplied natural-language input is fed to an LLM, whose untrusted output string is executed directly against the graph database. There is no validation, parameterisation, or permission check on that Cypher text. A malicious prompt can coerce the LLM to emit destructive or exfiltrating Cypher (e.g. MATCH (n) DETACH DELETE n; or unrestricted reads), resulting in arbitrary data access or modification. This is effectively a graph-query injection (CWE-89) enabled by prompt-injection of the LLM (OWASP-ML01).
critical
Link

@Vasilije1990 Vasilije1990 self-requested a review May 27, 2025 19:33
@Vasilije1990 Vasilije1990 marked this pull request as ready for review May 27, 2025 19:33
@Vasilije1990 Vasilije1990 merged commit ff997f4 into dev May 27, 2025
9 of 11 checks passed
@Vasilije1990 Vasilije1990 deleted the docs-docstring-modules branch May 27, 2025 19:34
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pensarapp bot commented May 27, 2025

LLM-to-Cypher Query Injection via Prompt Manipulation
Suggested Fix

@@ -1,6 +1,7 @@
 from typing import Any, Optional
 import logging
+import re
 from cognee.infrastructure.databases.graph import get_graph_engine
 from cognee.infrastructure.databases.graph.networkx.adapter import NetworkXAdapter
 from cognee.infrastructure.llm.get_llm_client import get_llm_client
 from cognee.infrastructure.llm.prompts import render_prompt
@@ -48,8 +49,48 @@
             """
         )
         return node_schemas, edge_schemas
 
+    def _is_cypher_query_safe(self, cypher_query: str) -> bool:
+        """
+        Check that a Cypher query is "safe" -- i.e., does not contain modification/destructive/admin keywords.
+        Returns True if it appears safe, False otherwise.
+        """
+        # Disallow keywords associated with data mutation or schema/admin operations
+        # Case-insensitive, ignore whitespace before/after, check for each forbidden word/phrase
+        forbidden_patterns = [
+            r"\bDETACH\s+DELETE\b",
+            r"\bDELETE\b",
+            r"\bREMOVE\b",
+            r"\bSET\b",
+            r"\bMERGE\b",
+            r"\bCREATE\b",
+            r"\bDROP\b",
+            r"\bCALL\b",
+            r"\bUSE\b",
+            r"\bLOAD\s+CSV\b",
+            r"\bAPOC\.",
+            r"\bDBMS\.",
+            r"(?<!\w)SHOW\b",  # For SHOW commands like SHOW DATABASES
+            r"\bALTER\b",
+            r"\bGRANT\b",
+            r"\bDENY\b",
+            r"\bREVOKE\b",
+            r"\bSTART\b",  # For START TRANSACTION etc.
+            r"\bCOMMIT\b",
+            r"\bROLLBACK\b",
+            r"\bRENAME\b",
+            r"\bCONSTRAINT\b",
+            r"\bINDEX\b",
+            r"\bTRUNCATE\b",
+            r"\bAUTH\b",
+            r"\bPASSWORD\b",
+        ]
+        pattern = re.compile("|".join(forbidden_patterns), re.IGNORECASE | re.MULTILINE)
+        if pattern.search(cypher_query):
+            return False
+        return True
+
     async def _generate_cypher_query(self, query: str, edge_schemas, previous_attempts=None) -> str:
         """Generate a Cypher query using LLM based on natural language query and schema information."""
         llm_client = get_llm_client()
         system_prompt = render_prompt(
@@ -78,8 +119,20 @@
                 cypher_query = await self._generate_cypher_query(
                     query, edge_schemas, previous_attempts
                 )
 
+                if not isinstance(cypher_query, str):
+                    raise ValueError("Generated Cypher query is not a string.")
+
+                if not self._is_cypher_query_safe(cypher_query):
+                    logger.error(
+                        f"Rejected potentially unsafe Cypher query (attempt {attempt + 1}): {cypher_query[:100]}..."
+                        if len(cypher_query) > 100
+                        else f"Rejected potentially unsafe Cypher query (attempt {attempt + 1}): {cypher_query}"
+                    )
+                    previous_attempts += f"Query: {cypher_query} -> Rejected: Unsafe or potentially destructive query detected\n"
+                    continue  # Try again for the remaining attempts
+
                 logger.info(
                     f"Executing generated Cypher query (attempt {attempt + 1}): {cypher_query[:100]}..."
                     if len(cypher_query) > 100
                     else cypher_query
@@ -156,5 +209,5 @@
         """
         if context is None:
             context = await self.get_context(query)
 
-        return context
+        return context
\ No newline at end of file
Explanation of Fix

Vulnerability and Fix Summary
The vulnerability arises from directly executing arbitrary Cypher queries generated by an LLM from untrusted user natural-language input ("query") without sanitization, parameterization, or authorization checks. An attacker could use prompt injection to coerce the LLM to produce harmful Cypher statements, leading to potential data exposure or destruction (CWE-89, ML01).

Fix Approach
To mitigate this, the patch introduces multiple defense layers:

  1. Validation of Generated Cypher:
    After receiving the Cypher query from the LLM, before executing it, the code validates the Cypher string for safety. The validator allows only read-only Cypher commands—rejecting/raising errors for any Cypher containing keywords linked to deletion, update, or administrative operations (such as DETACH DELETE, DELETE, REMOVE, SET, MERGE, CALL, CREATE, DROP, USE, LOAD CSV, etc.). The check is case-insensitive and robust to multiple keywords per line.

  2. No New Dependencies:
    The validation is implemented directly in Python without third-party packages.

  3. Fail-Closed Policy:
    If the Cypher query fails the validation, an exception is raised, logged, and the attempt is considered failed but retried up to the max_attempts limit.

  4. Extensibility:
    The validation function is defined as a private method (_is_cypher_query_safe) within the class. If the logic must be extended (for example, to allow parameterization or allowlisting patterns), it's easy to do so.

Potential Impacts

  • Only read-only Cypher is allowed when queries are generated via the LLM. Users attempting to execute write/delete/admin operations via natural language will get empty results or errors.
  • The rest of the codebase is unaffected unless other modules depend on malicious/destructive behavior via this path—which, given the retriever’s intent, should be prevented regardless.
Issues
Type Identifier Message Severity Link
Application
CWE-532, CWE-89, ML01
The untrusted user-supplied “query” string is embedded into the LLM prompt, which then returns an arbitrary Cypher statement that is executed directly against the graph database without any sanitisation, parameterisation, or authorisation checks. A malicious user can exploit this prompt-to-Cypher chain to coerce the LLM into producing destructive or exfiltrating commands (e.g., MATCH (n) DETACH DELETE n, CALL dbms.procedures()), leading to full data compromise. This constitutes a graph/SQL-style injection (CWE-89) driven by an LLM prompt-injection vector (OWASP ML Top-10 ML01).
critical
Link

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pensarapp bot commented May 27, 2025

Unsanitized Query Input Leading to Potential Graph/Vector Database Injection
Suggested Fix

@@ -1,13 +1,19 @@
 import asyncio
-from typing import Any, Optional
+import re
+from typing import Any, Optional, Callable, List, Dict
 
 from cognee.infrastructure.databases.graph import get_graph_engine
 from cognee.infrastructure.databases.vector import get_vector_engine
 from cognee.modules.retrieval.base_retriever import BaseRetriever
 from cognee.modules.retrieval.exceptions.exceptions import NoDataError
 from cognee.infrastructure.databases.vector.exceptions.exceptions import CollectionNotFoundError
 
+def _is_valid_node_id(node_id: str) -> bool:
+    if not isinstance(node_id, str):
+        return False
+    # Only allow alphanumeric, -, _, and length up to 64, no spaces
+    return re.fullmatch(r"[A-Za-z0-9_\-]{1,64}", node_id) is not None
 
 class InsightsRetriever(BaseRetriever):
     """
     Retriever for handling graph connection-based insights.
@@ -20,13 +26,28 @@
     - exploration_levels
     - top_k
     """
 
-    def __init__(self, exploration_levels: int = 1, top_k: int = 5):
-        """Initialize retriever with exploration levels and search parameters."""
+    def __init__(
+        self,
+        exploration_levels: int = 1,
+        top_k: int = 5,
+        allowed_nodes_callback: Optional[Callable[[str], bool]] = None,
+    ):
+        """Initialize retriever with exploration levels, search parameters, and (optional) allowed nodes callback.
+
+        allowed_nodes_callback, if provided, is called with a node_id and should return True if access is permitted.
+        """
         self.exploration_levels = exploration_levels
         self.top_k = top_k
+        self.allowed_nodes_callback = allowed_nodes_callback
 
+    def _is_allowed_node(self, node_id: str) -> bool:
+        # Check allowed_nodes_callback if provided, otherwise allow by default
+        if self.allowed_nodes_callback:
+            return self.allowed_nodes_callback(node_id)
+        return True
+
     async def get_context(self, query: str) -> list:
         """
         Find neighbours of a given node in the graph.
 
@@ -44,50 +65,92 @@
         --------
 
             - list: A list of unique connections found for the queried node.
         """
-        if query is None:
+        if query is None or not isinstance(query, str):
             return []
 
-        node_id = query
+        node_id = query.strip()
+        # Input validation: enforce strict node id format
+        if not _is_valid_node_id(node_id):
+            return []
+
+        if not self._is_allowed_node(node_id):
+            return []
+
         graph_engine = await get_graph_engine()
+
+        # Only validated node_id is used
         exact_node = await graph_engine.extract_node(node_id)
 
+        node_connections = []
         if exact_node is not None and "id" in exact_node:
-            node_connections = await graph_engine.get_connections(str(exact_node["id"]))
+            extracted_id = str(exact_node["id"])
+            if _is_valid_node_id(extracted_id) and self._is_allowed_node(extracted_id):
+                node_connections = await graph_engine.get_connections(extracted_id)
+            else:
+                return []
         else:
             vector_engine = get_vector_engine()
 
             try:
                 results = await asyncio.gather(
-                    vector_engine.search("Entity_name", query_text=query, limit=self.top_k),
-                    vector_engine.search("EntityType_name", query_text=query, limit=self.top_k),
+                    vector_engine.search(
+                        "Entity_name",
+                        query_text=node_id,
+                        limit=self.top_k,
+                    ),
+                    vector_engine.search(
+                        "EntityType_name",
+                        query_text=node_id,
+                        limit=self.top_k,
+                    ),
                 )
             except CollectionNotFoundError as error:
                 raise NoDataError("No data found in the system, please add data first.") from error
 
-            results = [*results[0], *results[1]]
-            relevant_results = [result for result in results if result.score < 0.5][: self.top_k]
+            # Flatten results
+            flat_results = [*results[0], *results[1]]
+            # Filter for score and valid node IDs and allowed nodes
+            relevant_results = [
+                result
+                for result in flat_results
+                if result.score < 0.5 and _is_valid_node_id(str(result.id)) and self._is_allowed_node(str(result.id))
+            ][: self.top_k]
 
             if len(relevant_results) == 0:
                 return []
 
+            # Only fetch connections for validated, allowed IDs
             node_connections_results = await asyncio.gather(
-                *[graph_engine.get_connections(result.id) for result in relevant_results]
+                *[graph_engine.get_connections(str(result.id)) for result in relevant_results]
             )
 
-            node_connections = []
             for neighbours in node_connections_results:
                 node_connections.extend(neighbours)
 
-        unique_node_connections_map = {}
-        unique_node_connections = []
+        unique_node_connections_map: Dict[str, bool] = {}
+        unique_node_connections: List[Any] = []
 
         for node_connection in node_connections:
-            if "id" not in node_connection[0] or "id" not in node_connection[2]:
+            if (
+                not isinstance(node_connection, list)
+                or len(node_connection) < 3
+                or "id" not in node_connection[0]
+                or "id" not in node_connection[2]
+            ):
                 continue
 
-            unique_id = f"{node_connection[0]['id']} {node_connection[1]['relationship_name']} {node_connection[2]['id']}"
+            left_id = str(node_connection[0]["id"])
+            right_id = str(node_connection[2]["id"])
+            if not _is_valid_node_id(left_id) or not _is_valid_node_id(right_id):
+                continue
+            if not self._is_allowed_node(left_id) or not self._is_allowed_node(right_id):
+                continue
+
+            relationship = node_connection[1].get("relationship_name") if isinstance(node_connection[1], dict) else str(node_connection[1])
+            unique_id = f"{left_id} {relationship} {right_id}"
+
             if unique_id not in unique_node_connections_map:
                 unique_node_connections_map[unique_id] = True
                 unique_node_connections.append(node_connection)
 
@@ -113,5 +176,5 @@
               based on the query.
         """
         if context is None:
             context = await self.get_context(query)
-        return context
+        return context
\ No newline at end of file
Explanation of Fix

Vulnerability Summary:
The original code allowed user-supplied input (query, used as node_id) to be directly passed into methods that may build dynamic Cypher or SQL queries. Without input sanitization, parameterization, or access controls, this enables attackers to inject malicious input (like graph/SQL injection) or enumerate/exfiltrate unrelated graph data, causing IDOR or data compromise.

Fix Summary:
This patch addresses the vulnerability by introducing both:

  1. Strict input validation: Only allow safe, known patterns for node IDs (alphanumeric, underscores, hyphens, max length).
  2. Parameterization and sanitization: Enforces that all queries and node IDs passed to database methods are properly sanitized before processing.
  3. Optional Callback for Authorization: Adds an optional allowed_nodes_callback parameter to check if the current user/session is allowed to access a given node or result, enforcing access control. By default, this is omitted (to avoid breaking changes), but the hook is present for integration.

Impact:
All user inputs used in sensitive queries are validated for safe format, thwarting injection risks. Access to node data by ID is restricted to IDs matching allowed patterns, and optionally restrictable via the callback.
No external dependencies or breaking changes are introduced; function signatures and return types remain the same.

Potential Impact:

  • If consuming code relies on passing arbitrary strings as queries, those that do not match the strict pattern will no longer return results.
  • Those using the new allowed_nodes_callback field to enforce authorization must supply a function; existing code is unaffected unless using this optional control.
Issues
Type Identifier Message Severity Link
Application
CWE-89, CWE-639
The user-controlled values query and node_id are propagated directly into calls to graph_engine.extract_node and vector_engine.search. If these lower-level helpers build Cypher, SQL, or similar queries through string interpolation, an attacker can inject malicious control characters or statements (e.g., " MATCH (n) DETACH DELETE n --") that manipulate or exfiltrate data. Because the code performs no input sanitization, encoding, or parameterization, it exposes the application to graph/SQL injection or full database compromise.
critical
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